1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 25 Phylogeny and Systematics

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Investigating the Tree of Life Phylogeny – Evolutionary history of a species or group of related species

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fossil record – Provides information about ancient organisms Figure 25.1

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Systematics uses – Morphological, biochemical, and molecular comparisons to infer evolutionary relationships Figure 25.2

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenies based on common ancestries inferred from fossil, morphological, and molecular evidence

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Fossil Record Sedimentary rocks – Richest source of fossils – Deposited into layers called strata Figure 25.3 1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils. Younger stratum with more recent fossils Older stratum with older fossils

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The fossil record – Based on the sequence in which fossils have accumulated in such strata Fossils reveal – Ancestral characteristics

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.4a–g (a) Dinosaur bones being excavated from sandstone (g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice (e) Boy standing in a 150-million-year-old dinosaur track in Colorado (d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber (b) Petrified tree in Arizona, about 190 million years old (c) Leaf fossil, about 40 million years old

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Organisms that share similar morphologies or similar DNA sequences – likely to be more closely related than organisms w/ different structures or sequences

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A potential misconception in constructing a phylogeny – Is similarity due to convergent evolution, called analogy, rather than shared ancestry

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Convergent evolution occurs when similar environmental pressures and natural selection – Produce similar (analogous) adaptations in organisms from different evolutionary lineages Figure 25.5

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evaluating Molecular Homologies Systematists use computer programs w hen analyzing comparable DNA segments from different organisms (sequence alignment) Figure 25.6 C C A T C A G A G T C C G T A Deletion Insertion C C A T C A A G T C C C C A T G T A C A G A G T C C C C A T C A A G T C C C C A T G T A C A G A G T C C 1 Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor. 2 Deletion and insertion mutations shift what had been matching sequences in the two species. 3Homologous regions (yellow) do not all align because of these mutations. 4Homologous regions realign after a computer program adds gaps in sequence 1. 1 2 1 2 1 2 1 2 A C G G A T A G T C C A C T A G G C A C T A T C A C C G A C A G G T C T T T G A C T A G Figure 25.7

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic systematics connects classification with evolutionary history Taxonomy – Division of organisms into categories based on a set of characteristics

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binomial nomenclature – Two-part format of the scientific name of an organism (Carolus Linnaeus)

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binomial name – Latinized – Genus and species

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hierarchical Classification Grouped in increasingly broad categories Figure 25.8 Panthera pardus Panthera Felidae Carnivora Mammalia Chordata Animalia Eukarya Domain Kingdom Phylum Class Order Family Genus Species

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Linking Classification and Phylogeny Shows evolutionary relationships –  branching phylogenetic trees Figure 25.9 Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Panthera Mephitis Lutra Canis FelidaeMustelidaeCanidae Carnivora Order Family Genus Species

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Each branch point – Represents the divergence of two species Leopard Domestic cat Common ancestor

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings “Deeper” branch points – Represent progressively greater amounts of divergence Leopard Domestic cat Common ancestor Wolf

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic systematics (trees) based on shared characteristics Cladogram – Depiction of patterns of shared characteristics among taxa Clade within a cladogram – Group of species that includes an ancestral species and all its descendants Cladistics – Study of resemblances among clades

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A valid clade is monophyletic – Signifying that it consists of the ancestor species and all its descendants Figure 25.10a (a)Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono- phyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics. Grouping 1 D C E G F B A J I K H

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In cladistic analysis – Clades are defined by their evolutionary novelties

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A shared primitive character – Homologous structure that predates the branching of a particular clade from other members of that clade

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A shared derived character – Evolutionary novelty unique to a particular clade

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Outgroup comparison – Focus on just those characters that were derived at the various branch points in the evolution of a clade Figure 25.11a, b

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Parsimony and Maximum Likelihood Can never be sure of finding the single best tree in a large data set Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Applying parsimony: Figure 25.14 Human MushroomTulip 40% 0 30% 0 Human Mushroom Tulip (a) Percentage differences between sequences 0

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Applying parsimony Figure 25.14 Tree 1: More likely (b) Comparison of possible trees Tree 2: Less likely 15% 5% 15% 20% 5% 10% 15% 25%

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.11 Constructing a cladogram Salamander TAXA Turtle Leopard Tuna Lamprey Lancelet (outgroup) 000 00 1 000 01 1 000 11 1 001 11 1 011 11 1 Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone) Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Turtle Salamander Tuna Lamprey Lancelet (outgroup) (a)Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. (b)Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny. CHARACTERS

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.12 Phylogram Drosophila Lancelet Amphibian Fish Bird Human Rat Mouse

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.13 Ultrametric tree Drosophila Lancelet Amphibian Fish Bird Human Rat Mouse Cenozoic Mesozoic Paleozoic Proterozoic 542 251 65.5 Millions of years ago

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.14 Trees with different likelihoods Human Tree 1: More likely Mushroom Tulip 40% 0 30% 0 0Human Mushroom Tulip (a) Percentage differences between sequences (b) Comparison of possible trees Tree 2: Less likely 15% 5% 15%20% 5% 10% 15% 25%

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The principle of maximum likelihood A tree can be found that reflects the most likely sequence of evolutionary events Figure 25.15a APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred. TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species. Species I Species II Species III Species IV I IIIIIIV I III II IV I II III Sites in DNA sequence Three possible phylogenetic hypothese 1 2 3 4 5 67 A GG G G G T G GG A G G G G A GG AA T G G A G A A G I II III IV IIIIIIIV AGGG G G G Bases at site 1 for each species Base-change event 1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here). 2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). 3 Now focus on site 1 in the DNA sequence. A single base- change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data. Species

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII GG AA GG AA GG AAGGAA GG AAGGAA GG TGTG T T T TTGG T G T TGGT T T T 10 events 9 events 8 events 4Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of these possible trees requires a total of four base-change events (marked again by crossbars). Thus, the first four sites in this DNA sequence do not help us identify the most parsimonious tree. 5 After analyzing sites 5 and 6, we find that the first tree requires fewer evolutionary events than the other two trees (two base changes versus four). Note that in these diagrams, we assume that the common ancestor had GG at sites 5 and 6. But even if we started with an AA ancestor, the first tree still would require only two changes, while four changes would be required to make the other hypotheses work. Keep in mind that parsimony only considers the total number of events, not the particular nature of the events (how likely the particular base changes are to occur). 6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data. RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.) Two base changes Figure 25.15b

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sometimes the best hypothesis is not the most parsimonious Figure 25.16a, b Lizard Four-chambered heart Bird Mammal Lizard Four-chambered heart Bird Mammal Four-chambered heart (a) Mammal-bird clade (b) Lizard-bird clade

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Much of an organism’s evolutionary history is documented in its genome  comparing nucleic acids(sequence alignment)  relatedness

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular clock – Yardstick for measuring evolutionary change based on observation that some genes appear to evolve at constant rates

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Example: Analysis shows that HIV is descended from viruses that infect other primates A comparison of HIV samples from throughout the epidemic has shown that the virus has evolved in a clocklike fashion

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Universal Tree of Life Divided into 3 great clades (domains): Bacteria, Archaea, and Eukarya The early history of 3 domains is not yet clear Figure 25.18 BacteriaEukaryaArchaea 4 Symbiosis of chloroplast ancestor with ancestor of green plants 3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 2Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells 1Last common ancestor of all living things LUCA 4 3 2 1 1 2 3 4 0 Billion years ago Origin of life